CURRICULUM VITAE Michael McClelland, Ph.D. Scientific Director, Vaccine Research Institute of San Diego Professor, University of California, Irvine, Adjunct. E-mail: mmcclell@uci.edu Website: http://www.vrisd.org/faculty.php?mcclelland EDUCATION Bristol University, England 1978 B.Sc., Biochemistry University of Georgia, Athens 1983 Ph.D., Molecular and Population Genetics EMPLOYMENT HISTORY 1978-1979 High School Teacher, Biology and Chemistry, Beverweerd, Netherlands. 1983-1984 Postdoctoral Fellow, Dept. Biochemistry U. California, Berkeley, CA 1984-1986 Markey Postdoctoral Fellow, Department of Genetics, Columbia University, NY 1986-1989 Markey Assistant Professor, Dept. Biochemistry Molecular Biology, U. Chicago, IL 1989-1995 Research Program Director, Cal. Inst. Bio. Res., La Jolla, CA 1995-2009 Professor, Sidney Kimmel Cancer Center, San Diego, CA. 2000-2011 U. California, San Diego, Cancer Center, Member. 2007-present Sanford Burnham Graduate School, San Diego, Adjunct Member. 2009-present Scientific Director, VRISD. Director, Genomics and Bioinformatics Cores. 2009-2011 Visiting Researcher, Dept. Pathology & Laboratory Medicine, U California, Irvine. 2011-present Adjunct Professor, Dept. Pathology & Laboratory Medicine, U California, Irvine. 2011-present U. California, Irvine, Cancer Center, Member. AWARDS/HONORS 1981,82,83 University-wide Predoctoral Research Fellowships, U. Georgia, Athens, GA 1983-1985 N.A.T.O. Postdoctoral Fellowship 1985-1989 Lucille P. Markey Biomedical Scholarship 1986-1989 Goldblatt Cancer Research Fund, Young Investigator 1992-2007 Editorial Board, Nucleic Acids Research 1995-1998 Member, NIH Genome Study section. 2005 Divisional lecture and award. ASM. 2011- Editorial Board, Prostate 2011- Editorial Board, Sequencing 2011- Editorial Board, International Journal of Microbiology Ongoing Five NIH P01 site visits. NCI Directors Challenge panel. Chair, Novel Technologies RFA

Study Section. Two Bioterrorism Center Grant reviews. Twelve NCI RFA and ad hoc panels. Three USDA and NSF panels. External reviewer for DOE, UK MRC, German DFG.

Current UCI committees

Center for Personalized Medicine, exploratory committee. Representing Pathology. Biorepository for Proactive Personalized Cancer Medicine, Pathology. Center for Genetics, exploratory committee. Representing Pathology and CPM. Research Program in Cancer Prevention and Prognosis, Cancer Center. Designated leader in prognosis. Hyundai Center Institute for childhood cancers. Scientific Advisory Board Hyundai Center Institute for childhood cancers. Tumor Board. Cooperating with Medical Informatics on an “honest broker” system and interest in BRAID. MitoMed: Working with Genetics and Pathology to ensure this service is not lost.

PREVIOUS COMMERCIAL EXPERIENCE Grants from New England Biolabs, and Boehringer Mannheim. Consultant for Stratagene, Diversa Corp, GenStar Corp, Clarity BioSciences, CIStem Corp. Consultant for venture capital companies on five financings.

Ad Hoc Consultant, Novartis, ClonTech. Founder of companies: Phenotypics, Proveri, ProArray, VivoCure. Licensed products to other companies. Co-PI on two funded SBIR grants. Nine patents awarded. Three patents pending. Two patents sold. GRANT SUPPORT PREVIOUS. Ten NIH R01 grants and competitive renewals as principal investigator. Ten other competitive research grants awarded as PI, including NSF and DOD. Eight previous grants awarded as co-PI. ACTIVE (Total costs to McClelland shown). U01 (Mercola) 09/01/10-10/01/15 1.8 cal mo NCI Early Detection Research Network. $150,000 Prostate cancer Biomarkers Role: Co-Principal Investigator. Major Goal: Improved detection of prostate cancer and improved prognosis. R01 AI077645-01 (Andrews) 06/01/09-11/30/13 1.2 cal mo NIH / National Institute of Allergy and Infectious Disease. $901,500 Identification of Salmonella Genes Involved in Persistence in Murine Intestine Role: Co-Principal Investigator. Major Goal: Identification of Salmonella genes involved in persistence in mice. Persistence is the main cause of contamination of animal products in human consumption. R01 AI039557-11 (Fang) 07/01/08-06/30/13 1.0 cal. mo. NIH / National Institute of Allergy and Infectious Disease. $200,000 Nitric Oxide Cytotoxicity in Salmonellosis. Role: Co-Principal Investigator. USDA (Teplitski) 06/01/10-05/30/13 0.6 cal. mo. Role: Co-Principal Investigator. $130,000 Salmonella interactions with tomatoes. Role: Co-Principal Investigator. USDA 2009-03579 (Andrews) 06/01/10-05/31/13 0.6 cal mo AFRI $89,000 Defining Salmonella Genes Important for Colonization and Persistence in Poultry Role: Co-Principal Investigator. Major Goal: Screening for Salmonella genes involved in infection and persistence in chickens. BARD (McClelland) 12/01/09-11/30/12 0.2 cal. mo. Role: Principal Investigator. $150,000 Major Goal: Desiccation resistance in bacteria. Renewal under submission. NIAID contract (McClelland) 10/01/10-06/01/13 1.2 cal mo NIH / National Institute of Allergy and Infectious Disease. $600,000 Fitness annotation of bacterial genomes Role: Principal Investigator. Major Goal: Generate fitness information in bacteria to be released in the PATRIC database. CPS (McClelland/Teplitski) 12/01/12–12/1/14 0.6 cal. mo. CPS $110,000 Role: Joint Principal Investigator. Avirulent Salmonella strains and their use to model behavior of the pathogen in water, composts, in and on vegetables. Major Goal: Safe models for food safety. OTHER SALARY SUPPORT UCI Cancer Center: Cancer Prevention and Prognosis. 7/01/12–06/30/13 1.2 cal. Mo.

Team leader in Etiology Center for Proactive Medicine. 7/01/12–06/30/13 0.6 cal. Mo. Deputy Leader OTHER CURRENT GRANTS SPONSORED R21 Grant to Nabil Arrach CIT Grant to Liz Chao Ph.D. Fellowship to Cecilia Silva GRANTS IN RENEWAL APPLICATION R01 AI083646-01 (Andrews) 07/01/09-06/30/12 1.2 cal mo NIH / National Institute of Allergy and Infectious Disease. $380,500 Identification of Salmonella Genes Important for Systemic Colonization Role: Co-Principal Investigator. Major Goal: Determining the complete set of genes that are required for systemic infection. This occurs in young, old, and immunocompromised humans and is a leading cause of death in Africa. Derivative new grant under submission. BC073899 (McClelland) 06/01/08-05/31/12 1.2 cal. mo. Department of Defense Breast Cancer Research Program $500,101 Engineering Improvements in a Bacterial Therapeutic Delivery System for Breast Cancer. Role: Principal Investigator Major Goal: Screen mutations in all non-essential genes in Salmonella to identify mutants that are unable to grow well in normal host tissues and screen for Salmonella promoters that are preferentially active in the breast tumor environment. Renewal under submission. R01 AI075093-01 (McClelland) 06/01/09-5/31/12 1.2 cal mo NIH / National Institute of Allergy and Infectious Disease. $730,000 Salmonella Genes Associated with Colonization of Specific Hosts Role: Principal Investigator. Major Goal: Manufacture of resource of all viable gene deletions. Use of this resource to the genes in Salmonella that are used in different hosts. Renewal under submission. R01 AI52237-04 (McClelland/Weinstock) 07/01/07–08/30/11 0.6 cal. mo. NIH / National Institute of Allergy and Infectious Disease. $584,400 Role: Joint Principal Investigator. A Resource for Salmonella Genome Sequencing. Major Goal: Sequencing bacterial genomes. Renewal under submission. PROFESSIONAL AFFILIATIONS Member; American Association for Cancer Research. Member; American Society for Microbiology. Member; American Society for Biochemistry and Molecular Biology THESIS COMMITTEES Two undergraduate thesis committees. Thirteen Ph.D. thesis committees. Ph.D. STUDENTS 1987-90 John Hanish, Ph.D. Patent Law, partner, New York. 1988-91 Mike Nelson, M.S. President Megabase Corp. 1995 Beat Schwitzer, B.S. Switzerland. 1998-1999 Anna Rojas, M.S. Assist. Prof, Madrid. 2003-04 Jon Alvarez Microbiology company in Spain. 2007 Kathrin Wolf, B.S. Biotech company in Germany. 2010 Nefise Akkoc Turkey Min. Education.

2011 Eduardo Morales Ph.D. Fellowship, Chile. 2010-current Cecilia Silva, M.S. Ph.D. Fellowship, Chile. POST-DOCS TRAINED: 1988-89 Bo-qin Qiang, M.D. Prof., Beijing, Member, Chinese Acad. Sci. 1988-90 Mike Weil, M.D. UCSF. 1988-90 Saibal Poddar, Ph.D. UCSD. 1989-90 Alvydas Spokauskas Biotech company in Vilnius. 1989-91 Bruno Sobral, Ph.D. Professor, Virginia Tech., Director Bioinformatics Institute. 1989-91 John Welsh, Ph.D. Associate Professor, VRISD. 1990-95 K.K. Wong, Ph.D. Associate Professor, M.D. Anderson, TX. 1991-94 David Ralph, Ph.D. Head lab at Urocor. 1991-95 Rhonda Honeycutt, Ph.D. CEO Clarity BioSci. 1992-93 Hartwig Arensdorf, Ph.D. Unknown location. 1993-97 Francoise Mathieu-Daude, Ph.D. WHO and Lavoisier Fellow. Now Assist. Prof., France. 1995-97 Thomas Vogt, M.D. DRG Fellow. Professor, head of department, U. Saarland. 1995-96 Frank Kullmann, M.D. DRG Fellow. Gastroenterology. Assist. Professor Regensburg. 1995-98 Nick Benson, Ph.D. Clinical Director Scripps Health. 1996-99 Barbara Jung, M.D. DRG Fellow. Assistant Professor, UCSD. 1996-99 Thomas Trenkle, M.D. DRG Fellow. Dr. Dental Surgery, Hamburg. 1998-00 Steven Ringquist, Ph.D. Assistant Professor, U. Pittsburgh 1999-01 David Boyle, Ph.D. Principal Investigator, Path.org 1999-01 Takuya Higashiyama, M.D. Kuma Hospital, Kobe, Japan. 1999-current Steffen Porwolik, Ph.D. Senior Researcher, VRISD 2000-09 Gaelle Rondeau, Ph.D. French Govt. Fellow. Senior researcher, VRISD. 2000-02 Gerhard Gerbauer, M.D. German Govt Fellow. Professor, U. Heidelberg. 2001-03 Jonathan Frye, Ph.D. Faculty, USDA, GA. 2001-10 YiPeng Wang, M.D. China Govt. Fellow. Program Director, Althea Oncology. 2001-03 Rosana Risques, Ph.D. Catalonia Govt. Fellow. Postdoc, U. Washington. 2003-04 QuiJu Yu, M.D. China Govt. Fellow. 2004-07 Carlos Santiviago, Ph.D. Chile Govt. Fellow. Assistant Professor in Chile. 2005-09 Nabil Arrach, Ph.D. Fellow. Now Sponsored junior faculty 2006 Eun-Ju Lee, M.D. Fellow, Seoul Korea. 2008-current Rocio Canals, Ph.D. Catalonia Govt. Fellow. 2008-09 Song, WenZhi, M.D. China Govt. Fellow. 2008-09 Kan, MuJie, M.D. China Govt. Fellow. 2009-11 Xiao-Qin Xia, Ph.D. China Govt. Fellow. Professor, Haibin, China. 2010-current Prerak Desai, Ph.D. Fellow 2010-11 Shabarinath Sreekumar, Ph.D. Postdoc in Ireland. 2010-11 Li Bie, M.D. China Govt. Fellow. Assistant Professor, China. 2010-12 Jennifer Guiterrez, Ph.D. Fellow. Postdoctoral fellow in France. 2011-12 Liz Chao, M.D. Sponsored junior faculty Visiting Scientists on extended Sabbaticals: 1993 P. Perolat, M.D. Professor, Pasteur. Three months. 1994-95 Richard Borowski, Ph.D. Professor, NYU. Six months. 1996-97 Kathrine Branger, Ph.D. Associate Professor, INSERM, Two years. 1996-97 Pierre Belichard, Ph.D. Sci. Fournier Inc., France. Six months. 2000-01 Catherine Legras, Ph.D. Professor, Lyon. One year. 2001-02 Javier Garaizar, Ph.D. Professor, Basque, Spain. Six months. 2003 Fidelma Boyd, Ph.D. Professor, U. Delaware. Three months. 2004 Silvana Spinelli, Ph.D ASM fellow, Argentina. Three months. 2004 Jerry Reen, Ph.D. Postdoc. Ireland. Three months. 2004 Raquel Quinera, Ph.D ASM fellow, Chile. Two months. 2004 Gopal Nath, M.D., Ph.D. Associate Professor, India. Six months. 2004 Erwin Strahsburger, Ph.D ASM fellow, Chile. Three months. 2005 Stephano Cairo, Ph.D. Fellow, Pasteur. Three months. 2005 Ed Schwartz, Ph.D. Prof. Germany. Five months. 2005 Jim Wilson, Ph.D. Fellow. Two months. 2005 Massimo Merighi, Ph.D. Fellow. Two months.

2005 Travis Bourrett, Ph.D. Fellow. Two months. 2005 GyeYung Yun, Ph.D. Fellow, Korea. Four months. 2005 Hyun-Joong Kim, Ph.D. Fellow. Two months. 2007-08 Sang-Ho Choi, Ph.D. Professor, Korea. Two years. 2007-08 Michael McConnell, Ph.D. Professor, USA, One year. 2010 Probadh Borah, Ph.D. Professor, U. of Assam. Six months. 2010 Lucas Pontel, Ph.D. ASM International Fellow, Argentina. Three months. 2010 Mudit Chandra, DVM Professor. Punjab Govt Fellow. Six months. Others: Charles Downing ASBMB sponsored high school teacher. Dan Howard ASBMB sponsored high school teacher. Teaching:

Biology laboratory, 101 and 102, nine quarters , UGA. Scientific literature circle, for graduate students and postdocs. Columbia University. Molecular Biology of the Cell. For Ph.D. and MSTP students. University of Chicago.

PEER-REVIEWED PUBLICATIONS (Citations updated in 2010) 1. Brown N, McClelland M, Whitehead P. 1980. HgiAI: A restriction endonuclease from Herpetosiphon

giganteus HP 1023. Gene 9:49-68. Citations: 24 2. McClelland M. 1981. The effect of sequence-specific DNA methylation on restriction endonuclease

cleavage. Nucleic Acids Research 9:5859-66. Citations: 97 3. McClelland M. 1981. Purification and characterization of two new modification methylases; M.ClaI

from Caryophanon latum L and M.TaqI from Thermus aquaticus YT1. Nucleic Acids Research 9:6795-804. Citations: 55

4. McClelland M, Ivarie R. 1982. Asymmetrical distribution of CpG in an "average" mammalian gene. Nucleic Acids Research 10:7865-77. Citations: 99

5. McClelland M. 1983. Frequency and distribution of methylatable DNA sequences in leguminous plant protein coding genes. J Molecular Evolution. 19:346-54. Citations: 31

6. McClelland M. 1983. The effect of site-specific methylation on restriction endonuclease cleavage. Nucleic Acids Research 11:r169-r173. Citations: 59

7. McClelland M, Kessler L, Bittner M. 1984. Site-specific cleavage of DNA at eight and ten base pair sequences. Proc. Natl. Acad. Sci. U.S.A. 81:983-98. Citations: 53

8. McClelland M, Nelson M. 1985. The effect of site-specific methylation on restriction endonuclease cleavage. Nucleic Acids Research 13:r201-r207. Citations: 81

9. McClelland M. 1985. Selection against dam methylation sites in the genomes of DNA enterobacteriophage. J Molecular Evolution. 21:317-322. Citations: 29

10. McClelland M, Nelson M, Cantor C. 1985. Purification of MboII methylase GAAGm6A) from Moraxella bovis: Site-specific cleavage of DNA at nine and ten base pair sequences. Nucleic Acids Research 13:7171-7182. Citations: 41

11. Brahmachari S, Souche Y, Cantor C, McClelland M. 1987. Sequences that adopt non-B-DNA conformation in form V DNA as probed by enzymic methylation. Journal Molecular Biology 193:201-211. Citations: 20

12. McClelland M, Jones R, Patel Y, Nelson M. 1987. Restriction endonucleases for pulsed field mapping of bacterial genomes. Nucleic Acids Research 15:5985-6005. Citations: 258

13. Nelson M, McClelland M. 1987. The effect of site-specific methylation on restriction-modification enzymes. Nucleic Acids Research 15:r219-r230. Citations: 62

14. McClelland M. 1987. Site-specific cleavage of DNA at 8-, 9-, and 10-bp sequences. Methods in Enzymology 155:22-25. Citations: 53

15. Nelson M, McClelland M. 1987. Purification and assay of type II DNA modification methylases. Methods in Enzymology 155:32-41. Citations: 11

16. McClelland M, Hanish J, Nelson M, Patel Y. 1988. KGB: A single type of buffer for all restriction endonucleases. Nucleic Acids Research 16:364. Citations: 108

17. McClelland M. 1988. Recognition sequences of Type II restriction systems are constrained by the G+C content of host genomes. Nucleic Acids Research 16:2283-2294. Citations: 18

18. Hanish J, McClelland M. 1988. Activity of restriction endonucleases and methylases in potassium glutamate (KGB). Gene Anal. Tech. 5:105-107. Citations: 30

19. McClelland M, Nelson M. 1988. The 5'-GGATCC-3' cleavage specificity of BamHI is increased to 5'-

CCGGATCCGG-3' by sequential double methylation with M.HpaII and M.BamHI. Gene 74:169-176. Citations: 11

20. McClelland M, Nelson M. 1988. The effect of site-specific DNA methylation on restriction endonucleases and DNA modification methyltransferases. Gene 74:291-304. Citations: 53

21. Nelson M, McClelland M. 1989. Effect of site-specific methylation on DNA modification methyltransferases and restriction endonucleases. Nucleic Acids Research 17:r389-r415. Citations: 45

22. Weil M, McClelland M. 1989. Enzymatic cleavage of a bacterial genome at a ten-base-pair recognition site. Proc. Natl. Acad. Sci. U.S.A. 86:51-55. Citations: 42

23. Patel Y, Nelson M, McClelland M. 1989. Methylation at overlapping E. coli. dam (Gm6ATC) sites does not block cleavage by the NruI (TCGCGA) isoschizomers AmaI, SalDI and SpoI. Nucleic Acids Research 17:3613. Citations: 2

24. Hanish J, McClelland M. 1989. Controlled partial restriction digestions of DNA by competition with modification methyltransferases. Analytical Biochem. 179:357-360. Citations: 8

25. Patel Y, Van Cott E, Wilson G, McClelland M. 1990. Cleavage at the twelve-base-pair sequence TCTAGATCTAGA using M.XbaI (TCTAGm6A) methylation and DpnI cleavage. Nucleic Acids Research 18:1603-1607. Citations: 9

26. Qiang B-Q, McClelland M, Poddar S, Spokauskas A, Nelson M. 1990. The apparent specificity of NotI (5'-GCGGCCGC-3') is enhanced by M.FnuDII and M.BepI methylases (5'-mCGCG-3'): Cutting bacterial chromosomes into a few large pieces. Gene 88:101-105. Citations: 16

27. Hanish J, McClelland M. 1990. Methylase-limited partial NotI cleavage for physical mapping of genomic DNA. Nucleic Acids Research 18:3287-3291. Citations: 15

28. Sobral B, Honeycutt R, Atherly A, McClelland M. 1990. Analysis of rice (Oryza sativa L.) genome using pulsed-field gel electrophoresis and rare-cutting restriction endonucleases. Plant Molecular Biology Rep. 8:252-274. Citations: 10

29. Welsh J, McClelland M. 1990. Fingerprinting genomes using PCR with arbitrary primers. Nucleic Acids Research 18:7213-7218. Citations: 5238.

30. Welsh J, Petersen C, McClelland M. 1991. Polymorphisms generated by arbitrarily primed PCR in the mouse: Application to strain identification and genetic mapping. Nucleic Acids Research 19:303-306. Citations: 362

31. Welsh J, McClelland M. 1991. Genomic fingerprints produced by PCR with consensus tRNA gene primers. Nucleic Acids Research 19:861-866. Citations: 167

32. Hanish J, McClelland M. 1991. Enzymatic Cleavage of a bacterial chromosome at a transposon-inserted rare site Nucleic Acids Research 19:829- 832. Citations: 13

33. Wong K, McClelland M. 1991. PCR with m5C replacing dCTP. Nucleic Acids Research 19:1081-1085. Citations: 17

34. Hanish J, Rebelsky, McClelland M, Westbrook C. 1991. Application of Methylase-limited partial NotI cleavage for physical mapping of the abl locus. Genomics 10:681-685. Citations: 7

35. Sobral, B, Honeycutt R, Atherly A, McClelland M. 1991. Electrophoretic separation of the three Rhizobium meliloti replicons. J Bacteriology 173:5173-5180. Citations: 74

36. Poddar S, McClelland M. 1991. Restriction Fragment Fingerprint and Genome Sizes of Staphylococcus Species Using Pulsed-Field Gel Electrophoresis and Infrequent Cleaving Enzymes. DNA Cell Biology 10:663-669. Citations: 10

37. Welsh J, McClelland M, Honeycutt R, Sobral B. 1991. Parentage determination in maize hybrids using arbitrarily primed PCR. Theoretical & Applied Genetics 82:473-476. Citations: 178

38. Welsh J, McClelland M. 1991. Genomic fingerprinting using arbitrarily primed PCR and a matrix of pairwise combinations of primers. Nucleic Acids Research 19:5275-5279. Citations: 271

39. Nelson M, McClelland M. 1991. Site-specific methylation: Effect on DNA modification methyltransferases and restriction endonucleases. Nucleic Acids Research 19:r2045-2071. Citations: 87

40. Nelson M, McClelland M. 1992. Use of DNA methyltransferase/endonuclease enzyme combinations for megabase mapping of chromosomes. Methods in Enzymology 216:279-303. Citations: 65

41. Sobral B, McClelland M. 1992. Methyltransferases as a tool to alter the specificity of restriction endonucleases. Methods in Molecular Biology 12:159- 172. Citations: 2

42. McClelland M, Nelson M. 1992. Effect of Site-specific methylation on DNA modification methyltransferases and restriction endonucleases. Nucleic Acids Research 20:r2145-2157. Citations: 49

43. McClelland M, Bhagwat A. 1992. Biased DNA repair. Correspondence. Nature 355:596-597. Citations: 12

44. Wong K, McClelland M. 1992. A BlnI restriction map of the Salmonella typhimurium LT2 genome. J Bacteriology 174:1656-61. Citations: 55

45. Honeycutt, R, Sobral, B, McClelland, M, Atherly A. 1992. Analysis of large DMA from soybean (Glycine max L. Merr.) by pulsed-field gel electrophoresis. Plant Journal. 2:133-135. Citations: 6

46. Welsh J, Pretzman C, Postic D, Saint Girons I, Baranton G, McClelland M. 1992. Genomic fingerprinting by arbitrarily primed PCR resolves Borrelia burgdorferi into three distinct groups. Int. J. Systematic Bacteriology 42:370-377. Citations: 190

47. Bhagwat A, McClelland M. 1992. DNA mismatch correction by Very Short Patch repair may have altered the abundance of oligonucleotides in the E. coli genome. Nucleic Acids Research 20:1663-1668. Citations: 42

48. McClelland M, Peterson C, Welsh J. 1992. Length polymorphisms in tRNA intergenic spacers detected using the polymerase chain reaction can distinguish streptococcal strains and species. J Clinical Microbiology 30:1499- 1504. Citations: 62

49. Poddar S, McClelland M. 1992. Nonspecific primer and PCR generated hybridization probes for physical ordering large restriction fragments in complex genome of Staphylococcus aureus. BBRC. 185:1055-61. Citations: 3

50. Wong K, McClelland M. 1992. Dissection of the Salmonella typhimurium genome by use of a Tn5 derivative carrying rare restriction sites. J Bacteriology 174:3807-11. Citations: 29

51. Welsh J, McClelland M. 1992. PCR-amplified length polymorphisms in tRNA intergenic spacers for categorizing staphylococci. Molecular Microbiology 6:1673-80. Citations: 49

52. Welsh J, Chada K, Dalal S, Ralph D, Cheng R, McClelland M. 1992. Arbitrarily primed PCR fingerprinting of RNA. Nucleic Acids Research 20:4965-70. Citations: 639

53. Nelson M, Raschke E, McClelland M. 1993. Effect of Site-Specific Methylation on Restriction Endonucleases and DNA Modification Methyltransferases. Nucleic Acids Research 21:3139-54. Citations: 193

54. Ralph D, McClelland M, Welsh J, Baranton G, Perolat P. 1993. Leptospira species categorized by arbitrarily primed polymerase chain reaction (PCR) and by mapped restriction polymorphisms in PCR-amplified rDNA. J Bacteriology 175:973-981. Citations: 118

55. Ralph D, Postic D, Baranton G, Pretzman C, McClelland M. 1993. Species of Borrelia distinguished by restriction site polymorphisms in 16S rRNA genes. FEMS Microbiology Lett. 111:239-244. Citations: 15

56. Al-Janabi S, Honeycutt R, McClelland M, Sobral B. 1993. A Genetic Linkage Map of Saccharum spontaneum L.SES 208'. Genetics. 134:1249-60. Citations: 102

57. Ralph D. Quideng Q, Van Etten J, McClelland M. 1993. Leptospira genomes are modified at 5'-GTAC. J Bacteriology 175:3913- 3915. Citation 2

58. Wong K, Mok C-H, Welsh J, McClelland M, Tsao S-W, Berkowitz R. 1993. Identification of differentially expressed RNA in human ovarian carcinoma cells by arbitrarily primed PCR fingerprinting of total RNAs. Int. J. Oncology 3:13-17. Citations: 26

59. Ralph D, McClelland M. 1993. A novel class of intervening sequences with conserved open reading frames found in eubacterial 23S rRNA genes. Proc. Natl. Acad. Sci. U.S.A. 90:6864-6868. Citations: 42

60. Fang F, McClelland M, Guiney D, Jackson M, Hartstein A, Morthland V, Davis C, McPherson D, Welsh J. 1993. Value of molecular epidemiologic analysis in a nosocomial methicillin-resistant Staphylococcus aureus outbreak. J American Medical Association 270:1323-8. [Commentary p1363]. Citations: 52

61. Ralph D, Welsh J, McClelland M. 1993. RNA fingerprinting using arbitrarily primed PCR identifies differentially regulated RNAs in Mink lung (Mv1Lu) cells growth arrested by TGF-b. Proc. Natl. Acad. Sci. U.S.A. 90:10710-10714. Citations: 101

62. Honeycutt R, McClelland M, Sobral B. 1993. Physical map of the genome of Rhizobium meliloti 1021. J Bacteriology 175:6945-6952. Citations: 86

63. McClelland M, Welsh J. 1994. DNA fingerprinting using arbitrarily primed PCR. Genome Research 4:S59-S65. Citations: 88

64. McClelland M, Welsh J. 1994. RNA fingerprinting using arbitrarily primed PCR. Genome Research 4:S66-S81. Citations: 84

65. Wong K, McClelland M. 1994. Stress-induced gene from Salmonella typhimurium identified by arbitrarily primed PCR of RNA (RAP). Proc. Natl. Acad. Sci. U.S.A. 91:639-643. Citations: 89

66. M McClelland, M Nelson, E Raschke. 1994. Effect of site-specific modification on restriction endonucleases and DNA modification methyltransferases. Nucleic Acids Research 22:3640-59. Citations: 282

67. McClelland M, Arensdorf H, Cheng R, Welsh J. 1994. Arbitrarily primed PCR fingerprints resolved on SSCP gels. Nucleic Acids Research 22:1770-1771. Citations: 27

68. Wong K, McClelland M. 1994. High-resolution restriction map for a 240-kilobase region spanning 91- to 96 minutes on the Salmonella typhimurium LT2 chromosome. J Bacteriology 176:5729-5734. Citations: 28

69. Ralph D, McClelland M. 1994. Phylogenetic evidence for horizontal transfer of an intervening sequence between species in a spirochete genus. J Bacteriology 176:5982-5987. Citations: 31

70. Al-Janabi S, McClelland M, Peterson C, Sobral B. 1994. Phylogenetic analysis of organellar DNA

sequences in the Andropogoneae: Saccharinae. Theoretical Applied Genetics 88:933-944. Citations: 82 71. Martinez I, Espelid S, Johansen A, Welsh J, McClelland M. 1994. Fast identification of species and

strains of Vibrio by amplification of polymorphic DNA. J Fish Diseases 17:297-302. Citations: 9 72. McClelland M, Ralph D, Cheng R, Welsh J. 1994. Interactions among regulators of RNA abundance

characterized using RNA fingerprinting by arbitrarily primed PCR. Nucleic Acids Research 22:4419-31. Citations: 44

73. Tigano-Milani M, Honeycutt R, Lacey L, Assie R, McClelland M, Sobral B. 1994. Genomic variability of Paecilomyces fumosoroseus strains revealed by molecular markers. J Invert. Pathology 65:274-282. Citations: 57

74. Dalal S, Welsh J, Tkachenko A, Ralph D, DiCicco-Bloom E, Bordas L, McClelland M, Chada K. 1994. Rapid isolation of tissue-specific and developmentally regulated brain cDNAs using RNA arbitrarily primed PCR (RAP-PCR). J Molecular Neuroscience 5:93-104. Citations: 14

75. Mathieu-Daude F, Welsh J, Tibayrenc M, McClelland M. 1995. Genetic diversity and population structure of Trypanosoma brucei: clonality versus sexuality. Molecular Biochem. Parasitology 72:89-101. Citations: 44

76. Honeycutt R, Sobral B, McClelland M. 1995. tRNA intergenic spacer reveal polymorphisms diagnostic for Xanthomonas albilineans. Microbiology 141:3229-39. Citations: 45

77. Borowsky R, McClelland M, R. Cheng, Welsh J. 1995. Arbitrarily primed DNA fingerprinting for phylogenetic reconstruction in vertebrates: The Xiphophorus model. Molecular Biology Evolution 12:1022-32. Citations: 69

78. Fukunaga M, Takahashi Y, Tsuruta Y, Matsushita O, Ralph D, McClelland M, Nakao M. 1995. Genetic and phenotypic analysis of Borrelia miyamoto sp. nov, isolated from the Ixodid tick Ixodes persulcatus, the vector for Lyme Disease in Japan. Int. Journal Systematic Bacteriology 45:804-10. Citations: 55

79. Kullmann F, McClelland M. 1995. Molecular genetics of gastric cancer (letter). New England Journal of Medicine 333:1427-8.

80. McClelland M, Mathieu Daude F, Welsh J. 1995. RNA fingerprinting and Differential display by arbitrarily primed PCR. Trends in Genetics 11:242-6. Citations: 238

81. Perucho M, Welsh J, Peinado M, Ionov Y, McClelland M. 1995. Fingerprinting of DNA and RNA by arbitrarily primed PCR: Application in Cancer Research. Methods in Enzymology 254:275-90. Citations: 32

82. Welsh J, Rampino N, McClelland M, Perucho M. 1995. Nucleic acid fingerprinting by PCR-based methods: applications to problems in aging and mutagenesis. Mutation Research 338:215-29. Citations: 33

83. Mathieu-Daude F, Cheng R, Welsh J, McClelland M. 1996. Screening of differentially amplified cDNA products from RNA arbitrarily primed PCR fingerprints using single strand conformation polymorphism (SSCP) gels. Nucleic Acids Research 24:1504-1507. Citations: 58

84. Mathieu-Daude F, Welsh J, Vogt T, McClelland M. 1996. DNA rehybridization during PCR: the “Cot effect’ and its consequences. Nucleic Acids Research 24:2080-2086. Citations: 87

85. Honeycutt R, Sobral B, McClelland M. 1997. Polymerase chain reaction (PCR) detection and quantification using a short PCR product and a synthetic internal positive control. Analytical Biochemistry 248:303-306. Citations: 5

86. Vogt T, Welsh J, Stolz W, Jung B, Kerbel R, Kobayashi H, Landthaler M, McClelland M. 1997. RNA fingerprinting displays UVB-specific disruption of transcriptional control in human melanocytes. Cancer Research 57:3554-3561. Citations: 30

87. Vogt T, Stolz W, Jung B, Welsh J, Kerbel R, Landthaler M, McClelland M. 1998. Overexpression of Lerk-5/Eplg5 mRNA: A Novel Marker for Increased Tumorgenicity and Metastatic Potential in Human Malignant Melanomas. Clinical Cancer Research 4:791-797. Citations: 68

88. Mathieu-Daude F, Welsh J, McClelland M. 1998. Differential gene expression during development in Trypanosoma brucei. Molecular Biochem. Parasitology 92:15-28. Citations: 11

89. Wong K, McClelland M, Stillwell L, Sisk E, Thurston S, Saffer J. 1998. Identification and Sequence Analysis of a 27-Kilobase Chromosomal Fragment Containing a Salmonella Pathogenicity Island Located at 92 Minutes on the Chromosome Map of Salmonella enterica Serovar Typhimurium LT2. Infection & Immunity 66:3365-71. Citations: 76

90. McClelland M, Wilson R. 1998. Comparison of Sample Sequences of the Salmonella typhi genome to the Sequence of the complete Escherichia coli K-12 genome. Infection & Immunity, 66:4305-12. Citations: 22

91. Schweitzer B, Taylor V, Welcher A, McClelland M, Suter U. 1998. Neural membrane protein 35 (NMP35): A novel member of a gene family, which is highly expressed in the adult nervous system. Molecular Cell Neurosci. 11:260-273. Citations: 25

92. Pesole G, Liuni S, Grillo G, Belichard P, Trenkle T, Welsh J, McClelland M, 1998. GeneUp: a program to

select short PCR primer pairs that occur in multiple members of sequence lists. BioTechniques 25:112-117. Citations: 12

93. Jung B, Vogt T, Mathieu-Daude F, Welsh J, McClelland M, Trenkle T, Weitzel C, Kullmann F. 1998. Estrogen-responsive RING finger mRNA induction in gastrointestinal carcinoma cells following bile acid treatment. Carcinogenesis 19:1901-6. Citations: 10

94. Trenkle T, Welsh J, Mathieu-Daude F, Jung B, McClelland M. 1998. Non-stoichiometric reduced complexity probes for cDNA arrays. Nucleic Acids Research 26:3883-91. Citations: 42

95. Mathieu-Daude F, Honeycutt R, Vogt T, Welsh J, McClelland M. 1998. Applications of DNA and RNA Fingerprinting by the Arbitrarily Primed Polymerase Chain Reaction. In: Bacterial Genomes: Physical Structure and Analysis. Citations: 32

96. Pardee A, McClelland M. (Editors) 1999. Expression Genetics I: Differential Display. Eaton Press. Citations: 11

97. Wong, M.-Y, Wong K, Benson N, McClelland M. 1999. Sample sequencing of a Salmonella typhimurium LT2 lambda library: Comparison to the E. coli K12 genome. FEMS Microbiology Lett. 173:411-23. Citations: 20

98. McClelland M, Pardee A. (Editors) 1999. Expression Genetics II: High Throughput Methods. Eaton Press. Citations: 11

99. Muller-Ladner U, Judex M, Justen H, Wessinghage D, Welsh J, McClelland M, Gay S, Scholmerich J, Kullmann F. 1999. Analysis of gene expression patterns in rheumatoid synovial fibroblasts using RAP-PCR for differential display. Med Klin. 94:228-32. Citations: 3

100. Mathieu-Daude F, Trenkle T, Welsh J, Jung J, Vogt T, McClelland M. 1999. Identification of differentially expresses genes using RNA fingerprinting by arbitrarily primed PCR. Methods in Enzymology 303:309-324. Citations: 14

101. Trenkle T, Mathieu-Daude F, Welsh J, McClelland M. 1999. Reduced Complexity probes for DNA arrays. Methods in Enzymology 303:380-392. Citations: 8

102. Trenkle T, Welsh J, McClelland M. 1999. Differential Display probes for cDNA arrays. BioTechniques 27:554-564. Citations: 22

103. Vogt T, Kroiss M, McClelland M, Gruss C, Becker B, Bosserhoff A, Rumpler G, Bogenrieder T, Landthaler M, Stolz. 1999. Deficiency of a novel retinoblastoma binding protein 2-homolog is a consistent feature of sporadic human melanoma skin cancer. Laboratory Invest. 79:1615-27. Citations: 17

104. Kullman F, Judex M, Ballhorn W, Justen H, Wessinghage D, Welsh J, Yen T, Lang B, Hittle J, McClelland M, Gay S, Scholmerich J, Muller-Ladner U. 1999. Kinesin-like protein CENP-E is upregulated in rheumatoid synovial fibroblasts. Arthritis Research 1:71-80. Citations: 17

105. Benson N, Wong M-.Y, McClelland M. 2000. Analysis of the SOS Response in Salmonella typhimurium Using RNA Arbitrarily Primed PCR. J Bacteriology 182:3490-97. Citations: 28

106. Trenkle T, McClelland M, Adlkofer K, Welsh J. 2000. Major transcript variants of VAV3, a new member of the VAV family of guanine nucleotide exchange factors. Gene 245:139-49. Citations: 21

107. Florea L, Riemer C, Schwartz S, Zhang Z, Stojanovic N, Miller W, McClelland M. 2000. Web-based visualization tools for bacterial genome alignments. Nucleic Acids Research 28:3486-96. Citations: 37

108. McClelland M, Florea L, Sanderson K, Clifton S, Wilson R, Miller W. 2000. Comparison of the E. coli K12 genome to sampled genomes of a Klebsiella pneumoniae and Salmonella enterica serovars Typhimurium, Typhi, and Paratyphi A. Nucleic Acids Research 28:4974-86. Citations: 69

109. Zeng L, Sachdev P, Yan L, Chan J, Trenkle T, McClelland M, Welsh J, Wang L. 2000. Vav3 mediates receptor protein tyrosine kinase signaling, regulates GTPase activity, modulates cell morphology, and induces cell transformation. Molecular Cell Biology 24:9212-24. Citations: 66

110. Glinsky G, Ivanova A, Welsh J, McClelland M. 2000. The role of blood group antigens in malignant progression, apoptosis resistance, and metastatic behavior. Transfus Med Rev. 4:326-50. Citations: 6

111. Porwollik S, Wong, M, Sims S, Schaaper R, DeMarini D, McClelland M. 2001. The delta-uvrB Mutations in the Ames Strains of Salmonella Span 15 to 119 Genes. Mutation Research 9246:1-11. Citations: 32

112. Vogt T, McClelland M, Jung B, Popova S, Bogenrieder T, Becker B, Rumpler G, Landthaler M, Stolz W. 2001. Progression and NSAID-induced apoptosis in malignant melanomas are independent of cyclooxygenase II. Melanoma Research 11:587-99. Citations: 40

113. McClelland M, Sanderson K, Spieth J, Clifton S, Latreille P, Courtney L, Ali J, Dante M, Du F, Hou S, Layman D, Leonard S, Nguyen C, Scott K, Holmes A, Grewal N, Mulvaney E, Ryan E, Sun H, Florea L, Miller W, Porwollik S, Stoneking T, Nhan M, Waterston R, Wilson R. 2001. Complete genome sequence of Salmonella enterica serovar Typhimurium LT2. Nature 413:852-6. Citations: 1148

114. Garaizar J, Porwollik S, Echeita A, Rementeria A, Herrera S, Wong R, Frye J, Usera M, McClelland M. 2002. DNA Microarray-Based Typing of an Atypical Monophasic Salmonella enterica Serovar. J Clinical Microbiology 40:2074-78. Citations: 47

115. Lechner S, Muller-Ladner U, Schlottmann K, Jung B, McClelland M, Ruschoff J, Welsh J, Scholmerich J,

Kullmann F. 2002. Bile acids mimic oxidative stress induced upregulation of thioredoxin reductase in colon cancer cell lines. Carcinogenesis 23:1281-8. Citations: 37

116. Porwollik S, Wong, M.-Y, McClelland M. 2002. Evolutionary genomics of Salmonella: Gene acquisitions revealed by microarray analysis. Proc. Natl. Acad. Sci. U.S.A. 99:8956-61. Citations: 179

117. Wilson J, Ott C, Ramamurthy R, Porwollik S, McClelland M, Pierson D, Nickerson C. 2002. Low-Shear Modeled Microgravity Alters the Salmonella enterica Serovar Typhimurium Stress Response in an RpoS-Independent Manner. Applied and Environmental Microbiology 68:5408-16. Citations: 30

118. Wilson J, Ramamurthy R, Porwollik S, McClelland M, Hammond T, Allen P, Ott C, Pierson D, Nickerson C. 2002. Microarray analysis identifies Salmonella genes belonging to the low-shear modeled microgravity regulon. Proc. Natl. Acad. Sci. U.S.A. 99:13807–13812. Citations: 45

119. Porwollik S, Frye J, Florea L, Blackmer F, McClelland M. 2003. A non-redundant microarray of genes for two related bacteria. Nucleic Acids Research 31:1869-76. Citations: 62

120. Florea L, McClelland M, Riemer C, Schwartz S, Miller W. 2003. EnteriX 2003: Visualization Tools for Genome Alignments of Enterobacteriaceae. Nucleic Acids Research 31:3527-32. Citations: 19

121. Porwollik S, McClelland M. 2003. Lateral Gene Transfer in Salmonella. Microbes & Infection 5:977-89. Citations: 43

122. Lawhon S, Frye J, Suyemoto M, Porwollik S, McClelland M, Altier C. 2003. Global regulation by CsrA in Salmonella Typhimurium. Molecular Microbiology 48:1633-45. Citations: 78

123. Boyd E, Porwollik S, Blackmer F, McClelland M. 2003. Differences in gene content among Salmonella enterica serovar Typhi isolates. J Clinical Microbiology 41:3823-8. Citations: 33

124. Bader M, Navarre W, Shiau W, Nikaido H, Frye J, McClelland M, Fang F, Miller S. 2003. Regulation of Salmonella typhimurium Virulence Gene Expression by Cationic Antimicrobial Peptides. Molecular Microbiology 50:219-30. Citations: 116

125. Ringquist S, Rondeau G, Risques RA, Higashiyama T, Wang YP, Porwollik S, Boyle D, McClelland M, Welsh J. 2003. Microarray analysis using RNA arbitrarily primed PCR. Methods Molecular Biology 226:245-54.

126. Rumpler G, Becker B, Hafner C, McClelland M, Stolz W, Landthaler M, Schmitt R, Bosserhoff A, Vogt T. 2003. Identification of differentially expressed genes in models of melanoma progression by cDNA array analysis: SPARC, MIF and a novel cathepsin protease characterize aggressive phenotypes. Experimental Dermatology 12:761-71. Citations: 27

127. Adamson E, De Belle I, Mittal S, Wang Y, Hayakawa J, Korkmaz K, O'Hagan D, McClelland M, Mercola D. 2003. Egr1 signaling in prostate cancer. Cancer Biol Ther. 2:610-6. Citations: 28

128. Alvarez A, Porwollik S, Laconcha I, Gisakis V, Belén Vivanco A, Gonzalez I, Echenagusia S, Zabala N, Blackmer F, McClelland M, Rementeria A, Garaizar J. 2004. Detection of a Salmonella enterica serovar California strain spreading in Spanish feedmills and its genetic characterization using DNA microarrays. Applied & Environmental Microbiology 69:7531-4. Citations: 15

129. Wang Q, Frye J, McClelland M, Harshey R. 2004. Gene expression patterns during swarming in Salmonella typhimurium: genes specific to surface growth and putative new motility and pathogenicity genes. Molecular Microbiology 52:169-87. Citations: 89

130. Porwollik S, Wong R, Helm A, Edwards K, Calcutt M, Eisenstark A, McClelland M. 2004. DNA Amplification and other Rearrangements in Archival Salmonella enterica serovar Typhimurium LT2 Cultures. J Bacteriology 186:1678-82. Citations: 18

131. Andrews-Polymenis HL, Rabsch W, Porwollik S, McClelland M, Rosetti C, Adams LG, Baumler AJ. 2004. Host Restriction of Salmonella enterica Serotype Typhimurium Pigeon Isolates Does Not Correlate with Loss of Discrete Genes. J Bacteriology 186:2619-2628. Citations: 12

132. Nair S, AlokamS, Kothapalli S, Porwollik S, Proctor E, Choy C, McClelland M, Liu S, Sanderson K. 2004. Salmonella enterica serovar Typhi strains from which SPI7, a 134 kb island with genes for Vi-exopolysaccharide and other functions, has been deleted. J Bacteriology 186:3214-23. Citations: 33

133. Rojas A, García de los Rios J, Fischer-Le Saux M, Jimenez P, Reche P, Bonneau S, Sutra L, Françoise Mathieu-Daudé F, McClelland M. 2004. Erwinia toletana sp. nov., associated with Pseudomonas savastanoi-induced tree knots. Int. Journal. System. Evolution. Microbiology 54:2217-22. Citations: 5

134. Porwollik S, Boyd EF, Choy C, Cheng P, Florea L, Proctor E, McClelland M. 2004. Characterization of Salmonella enterica subspecies I genovars using microarrays. J Bacteriology 186:5883–5898. Citations: 101

135. Cuadros C, Lopez-Hernandez F, Dominguez A, McClelland M, Lustgarten J. 2004. Flagellin fusion proteins as adjuvants or vaccines induce specific immune responses. Infection & Immunity 72:2810-6. Citations: 60

136. Helm A, Porwollik S, Stanley, Maloy S, McClelland M, Rabsch W, Eisenstark A. 2004. Pigeon-associated strains of Salmonella enterica serovar Typhimurium phage type DT2 have genomic rearrangements at ribosomal RNA operons. Infection & Immunity 72:7338-41. Citations: 3

137. Stuart R, Wachsman W, Berry C, Wang-Rodriguez J, Wasserman L, Klacansky I, Masys D, Arden K, Goodison S, McClelland M, Wang Y, Sawyers A, Kalcheva I, Tarin D, Mercola D. 2004. In silico dissection of cell-type associated patterns of gene expression in prostate cancer. Proc. Natl. Acad. Sci. USA. 101:615-20. Citations: 88

138. Hayakawa J, Mittal S, Wang Y, Korkmaz K, Adamson E, English C, McClelland M, Mercola D. 2004. Identification of genes bound and regulated by c-Jun and ATF2 transcription factors in vivo following DNA damage using promoter arrays. Molecular Cell 16:521-35. Citations: 80

139. McClelland M, Sanderson KE, Clifton SW, Latreille P, Porwollik S, Sabo A, Meyer R, Bieri T, Ozersky P, McLellan M, Harkins CR, Wang C, Nguyen C, Berghoff A, Elliott G, Kohlberg S, Strong C, Du F, Carter J, Kremizki C, Layman D, Leonard S, Sun H, Fulton L, Nash W, Miner T, Minx P, Delehaunty K, Fronick C, Magrini V, Nhan M, Warren W, Florea L, Spieth J, Wilson RK. 2004. Comparison of genome degradation in Paratyphi A and Typhi, human-restricted serovars of Salmonella enterica that cause typhoid. Nature Genetics 36:1268-74. Citations: 126

140. Frye J, Porwollik S, Blackmer F, Cheng P, McClelland M. 2004. Host gene expression changes and DNA amplification during temperate phage induction. J Bacteriology 187:1485-92. Citations: 24

141. Reen F, Boyd E, Porwollik S, Murphy B, Gilroy D, Fanning S, McClelland M. 2005. Genomic Comparisons of Salmonella enterica Serovar Dublin, Agona, and Typhimurium Strains Recently Isolated from Milk Filters and Bovine Samples from Ireland, Using a Salmonella Microarray. Applied & Environmental Microbiology 71:1616–25. Citations: 30

142. Jung B, Barbier V, Brickner H, Welsh J, Fotedar A, McClelland M 2005. Mechanisms of sulindac-induced apoptosis and cell cycle arrest. Cancer Lett. 219:15-25. Citations: 5

143. Monsieurs P, De Keersmaecker S, Navarre W, Bader M, De Smet F, McClelland M, Fang F, De Moor B, Vanderleyden J, Marchal K. 2005. Comparison of the PhoPQ regulon in Escherichia coli and Salmonella typhimurium. J. Molecular Evolution 60:462-74. Citations: 46

144. Navarre W, Halsey T, Walthers D, Frye J, McClelland M, Potter J, Kenney L, Gunn J, Fang F, Libby S. 2005. Co-Regulation of Salmonella enterica Genes Required for Virulence and Resistance to Antimicrobial Peptides by SlyA and PhoP/PhoQ. Molecular Microbiology 56:811-23. Citations: 86

145. Bang I-S, Frye J, McClelland M, Velayudhan I, Fang F. 2005. Alternative Sigma Factor Interactions in Salmonella E H Promote Antioxidant Defenses by Enhancing S Levels. Molecular Microbiology 56:492-508. Citations: 36

146. Morales C, Porwollik S, Frye J, Kinde H, McClelland M, Guard-Bouldin J. 2005. Correlation of phenotype with the genotype of egg-contaminating Salmonella enteritidis. Applied & Environmental Microbiology 71:4388-99. Citations: 29

147. Porwollik S, Santiviago C, Cheng P, Florea L, Jackson S, McClelland M. 2005. Differences in gene content between Salmonella enterica serovar Enteritidis isolates, and comparison to closely related serovars Gallinarum and Dublin. J Bacteriology 187:6545-55. Citations: 40

148. Wang Y, Yu Q, Cho A, Rondeau G, Welsh J, Adamson E, Mercola D, McClelland M. 2005. Survey of differentially methylated promoters in prostate cancer cell lines. Neoplasia 7:748-60. Citations: 45

149. Rondeau G, McClelland M, Nguyen T, Risques R, Wang Y, Judex M, Cho A, Welsh J. 2005. Enhanced microarray performance using low complexity representations of the transcriptome. Nucleic Acids Research 33:e100. Citations: 6

150. Xia X, McClelland M, Yipeng Wang Y. 2005. WebArray: an online platform for microarray data analysis. BMC Bioinformatics 6:306. Citations: 47

151. Faucher S, Porwollik S, Dozois C, McClelland M, Daigle F. 2006. Transcriptome of Salmonella enterica serovar Typhi within macrophages revealed through the selective capture of transcribed sequences. Proc. Natl. Acad. Sci. USA 103:1906-11. Citations: 57

152. Frye J, Karlinsey J, Felise H, Marzolf H, Dowidar N, McClelland M, Hughes K. 2006. Identification of new flagellar genes of Salmonella enterica serovar Typhimurium. J Bacteriology 188:2233-2243. Citations: 47

153. Frye J, Jesse T, Long F, Rondeau G, Porwollik S, McClelland M, Jackson C, Englen M, Fedorka-Cray P. 2006. DNA microarray detection of antimicrobial resistance genes in diverse bacteria. International J. Antimicrobial Agents 27:138-51. Citations: 33

154. Spence J, Duggan B, Eckhardt C, McClelland M. Mercola D. 2006. mRNAs Under Differential Translational Control in Ki-ras v-Ki-ras Transformed Cells. Molecular Cancer Research 4:47-60. Citations: 16

155. Risques R, Rondeau G, Judex M, McClelland M, Welsh J. 2006. Vertical arrays: microarrays of complex mixtures of nucleic acids. Methods Mol Biology 317:99-109. Citations: 1

156. Ledeboer N, Frye J, McClelland M, Jones B. 2006. Salmonella enterica serovar Typhimurium requires the Lpf, Pef, and Tafi fimbriae for biofilm formation on HEp-2 tissue culture cells and chicken intestinal epithelium. Infection & Immunity 74:3156-69. Citations: 23

157. Aguirre A, Cabeza M, Spinelli S, McClelland M, Garcia Vescovi E, Soncini F. 2006. PhoP-Induced Genes within Salmonella Pathogenicity Island 1. J Bacteriology 188:6889-98. Citations: 13

158. Wang Q, Mariconda S, Suzuki A, McClelland M, Harshey R. 2006. Uncovering a large set of genes that affect surface motility in Salmonella enterica serovar Typhimurium. J Bacteriology 188:7981-4. Citations: 13

159. Kang M, Besser T, Hancock D, Porwollik S, McClelland M, Call D. 2006. Identification of Specific Gene Sequences Conserved in Contemporary Epidemic Strains of Salmonella enterica. Applied & Environmental Microbiology 72:6938-47. Citations: 15

160. Faucher SP, Porwollik S, Dozois CM, McClelland M, Daigle F. 2006. Salmonella transcriptome during macrophage infection. Med Sci (Paris). 22:792-3.

161. Navarre W, Porwollik S, Wang Y, McClelland M, Salama N, Rosen H, Libby S, Fang F. 2006. Selective Silencing of Foreign DNA with Low GC Content by the H-NS Protein in Salmonella enterica Sv. Typhimurium. Science 313:236-8. Citations: 259

162. Fink RC, Evans MR, Porwollik S, Vazquez-Torres A, Jones-Carson J, Troxell B, Libby SJ, McClelland M, Hassan HM. 2007. FNR is a global regulator of virulence and anaerobic metabolism in Salmonella enterica serovar Typhimurium (ATCC 14028s). J Bacteriology 189:2262-73. Citations: 17

163. Thijs IM, De Keersmaecker SC, Fadda A, Engelen K, Zhao H, McClelland M, Marchal K, Vanderleyden J. 2007. Delineation of the Salmonella typhimurium HilA regulon through genome-wide location and transcript analysis. J Bacteriology 189:4587-96. Citations: 21

164. Wilson JW, Ott CM, Zu Bentrup KH, Ramamurthy R, Quick L, Porwollik S, Cheng P, McClelland M, Tsaprailis G, Radabaugh T, Hunt A, Fernandez D, Richter E, Shah M, Kilcoyne M, Joshi L, Nelman-Gonzalez M, Hing S, Parra M, Dumars P, Norwood K, Bober R, Devich J, Ruggles A, Goulart C, Rupert M, Stodieck L, Stafford P, Catella L, Schurr MJ, Buchanan K, Morici L, McCracken J, Allen P, Baker-Coleman C, Hammond T, Vogel J, Nelson R, Pierson DL, Stefanyshyn-Piper HM, Nickerson CA. 2007. Space flight alters bacterial gene expression and virulence and reveals a role for global regulator Hfq. Proc. Natl. Acad. Sci. USA. 104:16299-304. Citations: 48

165. Manna D, Porwollik S, McClelland M, Tan R, Higgins NP. 2007. Microarray analysis of Mu transposition in Salmonella enterica, serovar Typhimurium: transposon exclusion by high-density DNA binding proteins. Molecular Microbiology 66:315-28. Citations: 2

166. Thijs IM, De Keersmaecker SC, Fadda A, Engelen K, Zhao H, McClelland M, Marchal K, Vanderleyden I. 2007. Combining omics data to unravel the regulatory network controlling Salmonella invasion of epithelial cells. Commun Agric Appl Biol Sci. 72:55-9.

167. Ward WO, Swartz CD, Porwollik S, Warren SH, Hanley NM, McClelland M, DeMarini DM. 2007. Toxicogenomic analysis incorporating operon-transcriptional coupling and toxicant concentration-expression response: analysis of MX-treated Salmonella. BMC Bioinformatics 8:378. Citations: 5

168. Navarre W, McClelland M, Libby S, Fang F. 2007. Silencing of xenogenic DNA by H-NS – facilitation of lateral gene transfer in bacteria by a defensive system that recognizes foreign DNA. Genes & Development. 21:1456-1471. Citations: 59

169. Wang Q, Zhao Y, McClelland M, Harshey RM. 2007. The RcsCDB signaling system and swarming motility in Salmonella enterica serovar Typhimurium: dual regulation of flagellar and SPI-2 virulence genes. J Bacteriology 189:8447-57. Citations: 27

170. Porwollik S, McClelland M. 2007. Determination of the gene content of Salmonella genomes by microarray analysis. Methods Mol. Biology 394:89-103. Citations: 1

171. Singh V, Mishra S, Rao GR, Jain AK, Dixit VK, Gulati AK, Mahajan D, McClelland M, Nath G. 2008. Evaluation of nested PCR in detection of Helicobacter pylori targeting a highly conserved gene: HSP60. Helicobacter. 13:30-4. Citations: 9

172. Hoemme C, Peerzada A, Behre G, Wang Y, McClelland M, Nieselt K, Zschunke M, Disselhoff C, Agrawal S, Isken F, Tidow N, Berdel WE, Serve H, Muller-Tidow C. 2008. Chromatin modifications induced by PML-RAR-alpha repress critical targets in leukemogenesis as analyzed by ChIP-Chip. Blood. 111:2887-95. Citations: 15

173. Bourret TJ, Porwollik S, McClelland M, Zhao R, Greco T, Ischiropoulos H, Vazquez-Torres A. 2008. Nitric Oxide antagonizes the acid tolerance response that protects Salmonella against innate gastric defenses. PLoS ONE 3:e1833. Citations: 5

174. Scaria J, Raghavan Palaniappan UM, Chiu D, Phan JA, Ponnala L, McDonough P, Grohn Y, Porwollik S, McClelland M, Chiou C-S, Chu C, Chang YF. 2008. Microarray for molecular typing of Salmonella enterica serovars. Molecular & Cellular Probes. 22:238-43. Citations: 17

175. Arrach N, Zhao M, Porwollik S, Hoffman RM, McClelland M. 2008. Salmonella promoters preferentially activated inside tumors. Cancer Research 68:4827-32. Citations: 16

176. Risques R, Rondeau G, Judex M, McClelland M, Welsh, J. 2008. Assessment of gene expression in many samples using vertical arrays. Nucleic Acids Research 36:e60. Citations: 2

177. Arrach N, Porwollik S, Cheng P, Cho A, Long F, Choi S-H, McClelland M. 2008. Salmonella serovar identification using PCR-based detection of gene presence and absence. J. Clin. Microbiology 46:2581-9. Citations: 8

178. Koziol JA, Feng AC, Jia Z, Wang Y, McClelland M, Mercola D. 2009. The Wisdom of the Commons: Ensemble Tree Classifiers for Prostate Cancer Prognosis. Bioinformatics 25:54-60.

179. Papp-Wallace KM, Nartea M, Kehres DG, Porwollik S, McClelland M, Libby SJ, Fang FC, Maguire ME. 2008. The CorA Mg2+ channel is required for the virulence of Salmonella enterica serovar typhimurium. J Bacteriology 190:6517-23. Citations: 6

180. Wilson JW, Ott CM, Quick L, Davis R, zu Bentrup KH, Crabbé A, Richter E, Sarker S, Barrila J, Porwollik S, Cheng P, McClelland M, Tsaprailis G, Radabaugh T, Hunt A, Shah M, Nelman-Gonzalez M, Hing S, Parra M, Dumars P, Norwood K, Bober R, Devich J, Ruggles A, CdeBaca A, Narayan S, Benjamin J, Goulart C, Rupert M, Catella L, Schurr MJ, Buchanan K, Morici L, McCracken J, Porter MD, Pierson DL, Smith SM, Mergeay M, Leys N, Stefanyshyn-Piper HM, Gorie D, Nickerson CA. 2008. Media ion composition controls regulatory and virulence response of Salmonella in spaceflight. PLoS ONE. 3:e3923. Citations: 9

181. Arora S, Wang Y, Jia Z, Vardar-Sengul S, Munawar A, Doctor KS, Birrer M, McClelland M, Adamson E, Mercola D. 2008. Egr1 regulates the coordinated expression of numerous EGF receptor target genes as identified by ChIP-on-chip. Genome Biology 9:R166. Citations: 8

182. Xia XQ, McClelland M, Wang Y. 2009. Analyzing Microarray Data Using WebArray. Cold Spring Harbor Protocols PMID: 20147236

183. Ansong C, Yoon H, Porwollik S, Mottaz-Brewer H, Petritis BO, Jaitly N, Adkins JN, McClelland M, Heffron F, Smith RD. 2009. Global systems-level analysis of Hfq and SmpB deletion mutants in Salmonella: implications for virulence and global protein translation. PLoS ONE e4809. Citations: 20

184. Merighi M, Septer AN, Carroll-Portillo A, Bhatiya A, Porwollik S, McClelland M, John S Gunn JS. 2009. Genome-wide analysis of the PreA/PreB (QseB/QseC) regulon of Salmonella enterica serovar Typhimurium. BMC Microbiology 9:42. Citations: 8

185. Yoon H, McDermott JE, Porwollik S, McClelland M, Heffron F. 2009. Coordinated Regulation of Virulence during Systemic Infection of Salmonella enterica Serovar Typhimurium. PLoS Pathogens 5:e1000306. Citations: 18

186. Santiviago CA, Reynolds MM, Porwollik S, Choi SH, Long F, Andrews-Polymenis HL, McClelland M. 2009. Analysis of pools of targeted Salmonella deletion mutants identifies novel genes affecting fitness during competitive infection in mice. PLoS Pathogens 5:e1000477. Citations: 21

187. Xia XQ, McClelland M, Porwollik S, Song W, Cong X, Wang Y. 2009. WebArrayDB: Cross-platform microarray data analysis and public data repository. Bioinformatics 25:2425-9. Citations: 28

188. Frye JG, Lindsey RL, Rondeau G, Porwollik S, Long F, McClelland M, Jackson CR, Englen MD, Meinersmann RJ, Berrang ME, Davis JA, Barrett JB, Turpin JB, Thitaram SN, Fedorka-Cray PJ. 2010. Development of a DNA Microarray to Detect Antimicrobial Resistance Genes Identified in the National Center for Biotechnology Information Database. Microb Drug Resist. 16:9-19.

189. Lee EJ, McClelland M, Wang Y, Long F, Choi SH, Lee JH. 2010. Distinct DNA methylation profiles between adenocarcinoma and squamous cell carcinoma of human uterine cervix. Oncology Research 18:401-8.

190. O’Regan E, Quinn T, Frye JG, Pagès J-M, Porwollik S, Fedorka-Cray PJ, McClelland M, Fanning S. 2010. Fitness Costs and Stability of a High-Level Ciprofloxacin Resistance Phenotype in Salmonella enterica Serotype Enteritidis: Reduced Infectivity Associated with Decreased Expression of SPI-1 Genes. Antimicrobial Agents & Chemotherapy. 54:367-374.

191. Santiviago CA, Blondel CJ, Quezada CP, Silva CA, Tobar PM, Porwollik S, McClelland M, Andrews-Polymenis HL, Toro CS, Zaldívar M, Contreras I. 2010. Spontaneous excision of the Salmonella enterica serovar Enteritidis-specific defective prophage-like element {Phi}SE14. J Bacteriology 192:2246-54.

192. Kucerova E., Clifton SW, Xia X-Q, Long F, Porwollik S, Fulton L, Fronick C, Minx P, Kyung K, Warren W, Fulton R, Feng D, Wollam A, Shah N, Bhonagiri V, Nash W, Hallsworth-Pepin K, Wilson RK, McClelland M (corresponding author) and Forsythe SJ. 2010. Genome sequence of Cronobacter sakazakii BAA-894 and Comparative Genomic Hybridization analysis with other Cronobacter Species. PLoS ONE 5:e9556.

193. Arrach N, Cheng P, Zhao M, Santiviago CA, Hoffman RM, McClelland M. 2010. High-throughput screening for Salmonella avirulent mutants that retain targeting of solid tumors. Cancer Research 70:2165-70.

194. Xia XQ, Jia Z, Porwollik S, Long F, Hoemme C, Ye K, Müller-Tidow C, McClelland M, Wang Y. 2010. Evaluating oligonucleotide properties for DNA microarray probe design. Nucleic Acids Research 38:e121

195. Muller-Tidow C, Klein HU, Hascher A, Isken F, Tickenbrock L, Thoennissen N, Agrawal-Singh S, Tschanter P, Disselhoff C, Wang Y, Becker A, Thiede C, Ehninger G, Zur Stadt U, Koschmieder S, Seidl M,

Müller FU, Schmitz W, Schlenke P, McClelland M, Berdel WE, Dugas M, Serve H. 2010. Profiling of histone H3 lysine 9 trimethylation levels predicts transcription factor activity and survival in acute myeloid leukemia. Blood 116:3564-71

196. Thijs IM, Zhao H, De Weerdt A, Engelen K, De Coster D, Schoofs G, McClelland M, Vanderleyden J, Marchal K, De Keersmaecker SC. 2010. The AI-2-dependent regulator LsrR has a limited regulon in Salmonella Typhimurium. Cell Research 20:966-9

197. Xia XQ, McClelland M, Wang Y. 2010. TabSQL: a MySQL tool to facilitate mapping user data to public databases. BMC Bioinformatics 11:342

198. Noel JT, Arrach N, Alagely A, McClelland M, Teplitski M. 2010. Specific Responses of Salmonella enterica to Tomato Varieties and Fruit Ripeness Identified by In Vivo Expression Technology PLoS One 5:e12406.

199. Libby SJ, Brehm MA, Greiner DL, Shultz LD, McClelland M, Smith KD, Cookson BT, Karlinsey JE, Kinkel TL, Porwollik S, Canals R, Cummings LA, Fang FC. 2010. Humanized NOD-scid IL2rγ null Mice are Susceptible to Lethal Salmonella Typhi Infection. Proc. Natl. Acad. Sci. U.S.A. 107:15589-94.

200. Sheikh A, Charles RC, Rollins SM, Harris JB, Bhuiyan MS, Khanam F, Bukka A, Kalsy A, Porwollik S, Brooks WA, Larocque RC, Hohmann EL, Cravioto A, Logvinenko T, Calderwood SB, McClelland M, Graham JE, Qadri F, Ryan ET. 2010. Analysis of Salmonella enterica serotype Paratyphi A gene expression in the blood of bacteremic patients in Bangladesh. PLoS NTD 4: e908.

201. Andrews-Polymenis H, et al., 2011. Abrogation of the Twin Arginine Transport System in Salmonella enterica serovar Typhimurium Leads to Colonization Defects During Infection. PLoS One 6:e15800.

202. Cairo S, Wang Y, de Reyniès A, Duroure K, Dahan J, Redon MJ, Fabre M, McClelland M, Wang XW, Croce CM, Buendia MA. 2010. Stem cell-like micro-RNA signature driven by Myc in aggressive liver cancer. Proc. Natl. Acad. Sci. U.S.A. 107:20471-6.

203. Wang Y, Xia XQ, Zhenyu Jia Z, Anne Sawyers A, Yao H, Wang-Rodriquez J, Mercola D, McClelland M. 2010. In silico estimates of tissue components in surgical samples based on expression profiling data. Cancer Research 70:6448-55

204. Tickenbrock L, Klein HU, Trento C, Hascher A, Göllner S, Bäumer N, Kuss R, Agrawal S, Bug G, Serve H, Thiede C, Ehninger G, Stadt UZ, McClelland M, Wang Y, Becker A, Koschmieder S, Berdel WE, Dugas M, Müller-Tidow C; for the SAL (Study Alliance Leukemia) Group. 2011. Increased HDAC1 deposition at hematopoietic promoters in AML and its association with patient survival. Leuk Res. 35:620-625.

205. Evans MR, Fink RC, Vazquez-Torres A, Porwollik S, Jones-Carson J, McClelland M, Hassan HM. 2011. Analysis of the ArcA regulon in anaerobically grown Salmonella enterica sv. Typhimurium. BMC Microbiol. 11:58.

206. Weatherspoon-Griffin N, Zhao G, Kong W, Kong Y, Morigen, Andrews-Polymenis H, McClelland M, Shi Y. 2011. The CpxR/CpxA two-component system up-regulates two Tat-dependent peptidoglycan amidases to confer bacterial resistance to antimicrobial peptide. J Biol Chem. 286:5529-39.

207. Jia Z, Wang Y, Sawyers A, Yao H, Rahmatpanah F, Xia XQ, Xu Q, Pio R, Turan T, Koziol JA, Goodison S, Carpenter P, Wang-Rodriguez J, Simoneau A, Meyskens F, Sutton M, Lernhardt W, Beach T, Monforte J, (McClelland M; corresponding author), and Mercola D. 2011. Diagnosis of Prostate Cancer Using Differentially Expressed Genes in Stroma. Cancer Research 71:2476-2487.

208. Ansong C, Tolić N, Purvine SO, Porwollik S, Jones M, Yoon H, Payne SH, Martin JL, Burnet MC, Monroe ME, Venepally P, Smith RD, Peterson SN, Heffron F, McClelland M, Adkins JN. 2011. Experimental annotation of post-translational features and translated coding regions in the pathogen Salmonella Typhimurium. BMC Genomics 12:433.

209. Lamichhane-Khadka R, Frye JG, Porwollik S, McClelland M, Maier RJ. 2011. Hydrogen-Stimulated Carbon Acquisition and Conservation in Salmonella enterica serovar Typhimurium. J Bacteriol 193:5824-32.

210. Agrawal-Singh S, Isken F, Agelopoulos K, Klein HU, Thoennissen NH, Koehler G, Hascher A, Bäumer N, Berdel WE, Thiede C, Ehninger G, Becker A, Schlenke P, Wang Y, McClelland M, Krug U, Koschmieder S, Büchner T, Yu DY, Singh SV, Hansen K, Serve H, Dugas M, Müller-Tidow C. 2012. Genome wide analysis of histone H3 acetylation patterns in AML identifies PRDX2 as an epigenetically silenced tumor suppressor gene. Blood 119:2346-57. PMID: 22207736

211. Kaniuk NA, Canadien V, Bagshaw RD, Bakowski M, Braun V, Landekic M, Mitra S, Huang J, Heo WD, Meyer T, Pelletier L, Andrews-Polymenis H, McClelland M, Pawson T, Grinstein S, Brumell JH. 2011. Salmonella exploits Arl8B-directed kinesin activity to promote endosome tubulation and cell-to-cell transfer. Cell Microbiol. 13:1812-23. PMID: 21824248

212. Sheikh A, Charles RC, Sharmeen N, Rollins SM, Harris JB, Bhuiyan MS, Arifuzzaman M, Khanam F, Bukka A, Kalsy A, Porwollik S, Leung DT, Brooks WA, LaRocque RC, Hohmann EL, Cravioto A, Logvinenko T, Calderwood SB, McClelland M, Graham JE, Qadri F, Ryan ET. 2011. In vivo expression of Salmonella

enterica serotype Typhi genes in the blood of patients with typhoid fever in Bangladesh. PLoS Negl Trop Dis. 5:e1419. PMID: 22180799

213. Troxell B, Fink RC, Porwollik S, McClelland M, Hassan HM. 2011. The Fur regulon in anaerobically grown Salmonella enterica sv. Typhimurium: identification of new Fur targets. BMC Microbiol. 11:236. PMID: 22017966

214. Bie L, Zhao G, Cheng P, Rondeau G, Porwollik S, Ju Y, Xia XQ, McClelland M. 2011. The accuracy of survival time prediction for patients with glioma is improved by measuring mitotic spindle checkpoint gene expression. PLoS One. 6:e25631

215. Gal-Mor O, Suez J, Elhadad D, Porwollik S, Leshem E, Valinsky L, McClelland M, Schwartz E, Rahav G. 2012. Molecular and cellular hharacterization of a Salmonella enterica serovar Paratyphi A outbreak strain and the human immune response to infection. Clin Vaccine Immunol. 19:146-56. PMC3272918

216. Silva CA, Blondel CJ, Quezada CP, Porwollik S, Andrews-Polymenis HL, Toro CS, Zaldívar M, Contreras I, McClelland M, Santiviago CA. 2012. Infection of Mice by Salmonella enterica Serovar Enteritidis involves additional genes that are absent in the genome of serovar Typhimurium. Infect Immun. 80:839-49. PMID: 22083712

217. Karlinsey JE, Bang IS, Becker LA, Frawley ER, Porwollik S, Robbins HF, Thomas VC, Urbano R, McClelland M, Fang FC. 2012. The NsrR regulon in nitrosative stress resistance of Salmonella enterica serovar Typhimurium. Mol Microbiol. 85:1179-93. PMC3438343

218. Joseph S, Sonbol H, Hariri S, Desai P, McClelland M, Forsythe SJ. 2012. Diversity of the Cronobacter genus as revealed by multi locus sequence typing. J Clin Microbiol. PMC3421776

219. Joerger RD, Sartori C, Frye JG, Turpin JB, Schmidt C, McClelland M, Porwollik S. 2012. Gene expression Analysis of Salmonella enterica Enteritidis Nal(R) and Salmonella enterica Kentucky 3795 exposed to HCl and Acetic Acid in Rich Medium. Foodborne Pathog Dis. 9:331-7. PMC3353815

220. Morales EH, Calderón IL, Collao B, Gil F, Porwollik S, McClelland M, Saavedra CP. 2012. Hypochlorous acid and hydrogen peroxide-induced negative regulation of Salmonella enterica serovar Typhimurium ompW by the response regulator ArcA. BMC Microbiol. 12:63. PMC3358236

221. Hao LY, Willis DK, Andrews-Polymenis H, McClelland M, Barak JD. 2012. Requirement of siderophore biosynthesis for plant colonization by Salmonella enterica. Appl Environ Microbiol. 78:4561-70. PMCID: PMC3370490

222. Sabbagh SC, Lepage C, McClelland M, Daigle F. 2012. Selection of Salmonella enterica serovar Typhi genes involved during interaction with human macrophages by screening of a transposon mutant library. PLoS One. 7:e36643. PMC3344905

223. Swearingen MC, Porwollik S, Desai PT, McClelland M, Ahmer BM. 2012. Virulence of 32 Salmonella strains in mice. PLoS One. 7:e36043. PMID: 225583201.

224. Grim CJ, Kothary MH, Gopinath G, Jarvis KG, Beaubrun JJ, McClelland M, Tall BD, Franco AA. 2012. Identification and characterization of Cronobacter iron acquisition systems. Appl Environ Microbiol. 78:6035-50. PMID: 22706064

225. Canals R, Xia XQ, Fronick C, Clifton SW, Ahmer BM, Andrews-Polymenis HL, Porwollik S, McClelland M. 2012. High-throughput comparison of gene fitness among related bacteria. BMC Genomics. 13:212. PMID: 22646920

226. Jia Z, Wang Y, HuY, McLaren C, Yu Y, Ye K, Xia XQ, Koziol JA, Lernhardt W, McClelland M, Mercola D. 2012. A sample selection strategy to boost the statistical power of signature detection in cancer expression profile studies. Anti-Cancer Agents in Medicinal Chem, 13, (in press) PMID: 22934703

227. Gruzdev N, McClelland M, Porwollik S, Ofaim S, Pinto R, Saldinger-Sela S. 2012. Global transcriptional analysis of dehydrated Salmonella enterica serovar Typhimurium. Appl Environ Microbiol. 2012 Aug 31. PMID: 22941081

228. Periaswamy B, Maier L, Vishwakarma V, Slack E, Kremer M, Andrews-Polymenis HL, McClelland M, Grant AJ, Suar M, Hardt WD. 2012. Live Attenuated S. Typhimurium Vaccine with Improved Safety in Immuno-Compromised Mice. PLoS One. 7:e45433. PMID: 23029007.

229. Jia Z, Rahmatpanah FB, Chen X, Lernhardt W, Wang Y, Xia XQ, Sawyers A, Sutton M, McClelland M (joint corresponding author), Mercola D. 2012. Expression changes in the stroma of prostate cancer predict subsequent relapse. PLoS One. 7:e41371. PMC3411675

230. Chen X, Xu S, McClelland M, Rahmatpanah F, Sawyers A, Jia Z, Dan Mercola D. 2012. An accurate prostate cancer prognosticator using a Seven-Gene signature -plus Gleason score and taking cell type heterogeneity into account. PLoS One. 7:e45178. PMID: 23028830

231. Kullas A, McClelland M, Yang HJ, Tam J, Torres A, Porwollik S, Mena P, McPhee J, Bogomolnaya L, Andrews-Polymenis H, van der Velden A. 2012. Salmonella utilize L-asparaginase II to inhibit the response of mammalian T cells. Cell Host & Microbes (in press).

BOOKS AND BOOK CHAPTERS 1. Nelson M, McClelland M. 1987. Enhancement of the apparent specificities of restriction endonucleases:

Applications to megabase mapping. In: Gene Amplification & Analysis. Volume V. Ed: Chirikjian J. Elsevier N.Y. Chapter 10:257-282. Citations: 15

2. Cantor C, Bandopadhaya S, Brahmachari S, Hui C, McClelland M, Morse M. 1988. Torsional stress, Unusual DNA structures; and Eukaryotic gene expression. In: Unusual DNA structure”; Eds. Wells R, Harvey S. Springer-Verlag, New York.

3. McClelland M. 1991. Site-specific methylation. Molecular Biology LabFax, Bios scientific publishers, pp126-138. 4. Welsh J, McClelland M. 1991. Applications of PCR-based genomic fingerprinting to genetic mapping, population

biology and epidemiology. Juan March Foundation, Madrid, Spain 263:65-68. 5. Welsh J, McClelland M. 1993. The characterization of pathogenic microorganisms by genomic fingerprinting

using arbitrarily primed polymerase chain reaction (AP-PCR). In: Diagnostic Molecular Microbiology. Eds: Persing D, Smith T, Tenover F, White T. ASM Press Washington D.C. pp595-602. Citations: 38

6. McClelland M, Chada K, Welsh J, Ralph D. 1993. Arbitrary primed PCR fingerprinting of RNA applied to mapping differentially expressed genes. In: DNA fingerprinting: State of the Science. Symposium: November 9th (1992) Eds: Pena S, Charkraborty R, Epplen J, Jeffreys, A. Birkhauser Verlag, Basel/Switzerland. Citations: 24

7. Welsh J, Wong R, Arvidson D, Arvidson C, McClelland M. 1993. Arbitrarily primed PCR generates fingerprints that can be used in genetic mapping, phylogenetics and population biology: Application to brewing yeasts. PCR: an in vitro replication process. Ed: Larzul. D. Intercept, London, U.K.

8. Welsh J, Petersen C, McClelland M. 1993. PCR of tRNA intergenic regions can be used as a diagnostic method to classify species of bacteria. PCR: an in vitro replication process. Ed. D. Larzul. Intercept, London, U.K.

9. Ralph D, McClelland M. 1994. Mapped restriction site polymorphisms (MRSPs) in PCR products for rapid identification and classification of genetically distinct organisms. In: PCR Technology: Current Innovations. Eds: Giffin H, Griffin A. CRC Press. Citations: 3

10. Welsh J, Ralph D, McClelland M. 1994. DNA and RNA fingerprinting using arbitrarily primed PCR. In: PCR Strategies. Eds: Sninsky J. et al,. 249-76. Citations: 28

11. Liu, S.-L, Wong K, McClelland M, Sanderson K. 1993. The construction of a physical map of the genome of Salmonella typhimurium. 'The Biology of Salmonella", Eds: Cabello F, Hormaeche C, Mastroeni P, Bonina L. Plenum Press, NY. Citations: 3

12. Welsh J, Perucho M, Peinado M, Ralph D, McClelland M. 1995. Fingerprinting of DNA and RNA by arbitrarily primed polymerase chain reaction: applications in cancer research. In: PCR II - A Practical Approach. Eds. McPherson M, Hames B, Taylor G, IRL Press, Oxford, New York. pp 197-218. Citations: 31

13. Honeycutt R, McClelland M. 1995. Molecular tools for pathogen detection. In: The Impact of Plant Molecular Biology. Ed: Sobral B. Birkhauser: Boston pp 187-201.

14. Wong K, Cheng R, Ralph D, Welsh J, McClelland M. 1995. DNA fingerprinting by Arbitrarily primed PCR (RAPDs). In: Molecular Microbial Ecology Manual. Chapter 3.4.2. Eds: Akkermans AL, van Elas J, de Bruijn F. Klewer Academic publishers. Citations: 6

15. Honeycutt R, Welsh J, McClelland M. 1995. PCR of tRNA intergenic regions can be used as a diagnostic method to classify species of bacteria. In: PCR: Procedures for in vitro replication. Ed: Larzul D. Intercept: London.

16. Welsh J, McClelland M. 1995. Arbitrarily primed PCR for genomic fingerprinting: application to genetic mapping, population biology and epidemiology. In: The Polymerase chain reaction. Eds: Ferre F, Mullis K, Gibbs R, Ross A. Published by Birkhauser-Springer-Verlag. Citations: 6

17. Chada K, Welsh J, McClelland M. 1996. RNA fingerprinting by arbitrarily primed PCR. In: A laboratory guide to RNA: Isolation, analysis, synthesis. Ed. Krieg P. John Wiley & Sons, New York.

18. Honeycutt R, McClelland M. 1996. Application of the Polymerase Chain Reaction to the Detection of Plant Pathogens. In: The Impact of. Plant Molecular Genetics. Ed: Sobral BWS. Birkhauser. Citations: 3

19. Arribas R, Tortola S, Welsh J, McClelland M, Peinado M. 1996. Arbitrarily primed PCR and RAPDs. In: Springer Lab Manual. Eds: Micheli M, Bova R. Springer Verlag. Citations: 6

20. Arribas R, Tortola S, Welsh J, McClelland M, Peinado M. 1996. Analysis of tumor-specific alterations by Arbitrarily primed PCR. In: Springer Lab Manual. Eds: Micheli M, Bova R.. Springer Verlag.

21. Ricote M, Welsh J, McClelland M. 1996. RNA Arbitrarily primed PCR (RAP-PCR). In: Springer Lab Manual. Eds: Micheli M, Bova R. Springer Verlag.

22. McClelland M, Sanderson K, Wong K. 1997. Rare cleavage strategies for bacterial mapping. In: Bacterial Genomes. Eds: DeBruijn F, Lupski J, Weinstock G. Publisher: Chapman & Hall. Citations: 2

23. Sanderson K, Hessel A, McClelland M, Liu S.-L. 1997. The physical map of Salmonella typhimurium. In: Bacterial Genomes. Eds: DeBruijn F, Lupski J, Weinstock G. Publisher: Chapman & Hall.

24. Vogt T, Welsh J, Mathieu-Daude F, Kullmann F, McClelland M, 1997. Fingerprinting of DNA and RNA using arbitrarily primed PCR. In: Eds: Caaetano-Anolles G, Gresshoff P. Citations: 2

25. McClelland M, Honeycutt R, Mathieu-Daude F, Vogt T, Welsh J. 1997. Fingerprinting by arbitrarily primed PCR. In: Differential Display Methods and Protocols. Liang & Pardee, Eds. Humana Press. Citations: 10

26. Ralph D, McClelland M. 1998. Arbitrarily primed PCR methods for studying bacterial diseases. In: Molecular Bacteriology: Protocols and Clinical Applications. Eds: Wooford N, Johnson A, Humana Press, Totowa, NJ. Citations: 4

27. Mathieu-Daude F, Benson N, Kullmann F, Honeycutt R, McClelland M, Welsh J. 1999. Screening differential displayed PCR products by single-stranded conformation polymorphism gels. In: PCR Applications: protocols for genomics. Eds, Innis M, Gelfand D, Sninsky J, Academic Press. Citations: 2

28. Jung B, Trenkle, T. McClelland M, Mathieu-Daude F, Welsh J. 1999. PCR5: Differential Display: a practical approach. In: Eds: Leslie R, Robertson H. Oxford University Press. Citations: 22

29. Sanderson K, McClelland M, Liu S. 1999. Stable Genomes. Organization of the Prokaryote Genome. Ed. Charlebois R. ASM, Washington, D.C.

30. Ringquist S, Trenkle T, Welsh J, McClelland M. 2000. Arbitrarily primed PCR probes for cDNA arrays. In: Methods in Molecular Medicine. Ed: Stirling D. Humana Press.

31. Wang Y, Hayakawa J, Long F, Yu Q, Cho A, Rondeau G, Welsh J, Mittal S, De Belle I, Adamson E, McClelland M, Mercola D. 2005. “Promoter Array” studies identify cohorts of genes directly regulated by methylation, copy number change, or transcription factor binding in human cancer cells. Annals NYAS 1058:162-185. Citations: 7

32. Andrews-Polymenis H, Santiviago C, McClelland M. 2009. Novel genetic tools for studying food borne Salmonella. Current Opinions in Biotechnology 20:149-57. Citations: 7

33. Canals R, McClelland M, Santiviago CA, and Andrews-Polymenis H, 2011. Genomics of Salmonella Species. Foodborne Bacterial Pathogens. Food Microbiology and Food Safety, 171-235.

34. Reynolds MM, Canals R, McClelland M, Andrews-Polymenis H. 2011. High-throughput screening to determine the genetic requirements for Salmonella survival under different growth conditions. In: Salmonella: From Genome to Function. S. Porwollik, Editor. Caister Academic Press.

35. Chen X, Xu S, Wang Y, McClelland M, Jia, Z, Mercola, D. 2011. Identification of Biomarkers for Prostate Cancer Prognosis Using a Novel Two-Step Cluster Method. Pattern Recognition in Bioinformatics. Springer-Verlag New York Inc.

Patents

1. 4,808,525 Site specific cleavage of DNA 2. 5,437,975 Consensus sequence primed polymerase chain reaction method for

fingerprinting genomes 3. 5,487,985 Arbitrarily primed polymerase chain reaction method for fingerprinting genomes 4. 6,495,319 Reduced complexity nucleic acid targets and methods of using same 5. 6,566,053 Identification of neoplasms by detection of genetic insertions and deletions 6. 6,599,701 Identifying organisms by detecting intronic nucleic acids 7. 6,696,277 Arbitrarily primed polymerase chain reaction method for fingerprinting genomes 8. 7,090,978 Identification of neoplasms by detection of genetic insertions and deletions 9. 7,816,080 Identifying organisms by detecting intronic nucleic acid or encoded proteins 10. 20110195847 Methods to treat solid tumors 11. 20110236903 Materials and methods for determining diagnosis and prognosis of prostate

cancer. 12. Pending. The accuracy of survival time prediction for patients with Glioma is improved by

measuring Mitotic Spindle Checkpoint gene expression Major data deposits not covered in the publications listed above: 13. McClelland M, Sanderson E, Porwollik S, Spieth J, Clifton S, Fulton R, Chunyan W, Wollam A, Shah N, Pepin K,

Bhonagiri V, Nash W, Johnson M, Thiruvilangam P, Wilson R (2008) Salmonella enterica subsp. arizonae serovar 62:z4,z23:--, complete genome. GenBank CP000880.

14. McClelland M, Sanderson E, Spieth J, Clifton S, Latreille P, Sabo A, Pepin K, Bhonagiri V, Porwollik S, Ali J, Wilson R (2007) Klebsiella pneumoniae subsp. pneumoniae MGH 78578, complete sequence. GenBank CP000647 5315120 bp.

15. McClelland M, Sanderson E, Porwollik S, Spieth J, Clifton S, Fulton R, Cordes M, Wollam A, Shah N, Pepin K, Bhonagiri V, Nash W, Johnson M, Thiruvilangam P, Wilson R (2007) Salmonella enterica subsp. enterica serovar Paratyphi B str. SPB7, complete genome. GenBank CP000886 4858887 bp.

Michael McClelland. Brief synopsis of past research accomplishments My research interests are in two areas of molecular biology. First, I have long focused on the evolution of pathogenesis, and diagnostics, with Salmonella as the model. Previous work includes: (1) Publication of the first Salmonella genome, and the release of hundreds of additional genomes to the public, prior to publication. (2) Development of the first whole-genome arrays for Salmonella and web-based methods for analysis of array data. Over 200 experiments have been made publicly available. (3) The first genome-based descriptions of Salmonella phylogeny using all genes, including the discovery of genomovars in this genus (genome variants within the same serovar). (4) The discovery of the role of H-NS as a universal regulator of virulence. (5) The systematic deletion of each individual gene and multigene islands in Salmonella enterica serovar Typhimurium 14028, to facilitate world-wide multi-faceted genetic studies on this model, and to enhance systems biology efforts. Second, I have a long-standing interest in improving cancer diagnostics, prognostics, and treatment. I have engineered Salmonella to improve its natural ability as a tumor targeting and delivery agent. Over the last ten years, I have been involved in many clinical translation projects including the discovery of the first stromal biomarkers associated with cancer diagnosis and progression in prostate cancer. In other work, I was the first to discover CpG islands, developed the first megabase DNA cleavage tools, and invented Arbitrarily Primed PCR, a simple genome fingerprinting tool, which has been used in many thousands of papers in population biology and in the discovery of the mutator phenotype in cancer. I was closely involved in the invention of ChIP–on-chip technology. I developed a variety of bioinformatics tools used for genome analysis. My work has been cited over 18,000 times. I have supervised 35 students and postdoctoral fellows, the majority of whom have gone on to successful academic and industrial careers. Michael McClelland. Brief synopsis of current research Program 1: Salmonella Genomics. Background. Salmonellae are among the most important orally acquired pathogens in the world. Approximately one million deaths and 100 million human infections are caused annually by these organisms, and they are major pathogens of domestic livestock. On a genomic level, strains within this species can differ by hundreds of their ~4,500 genes. This variability is the result of a mosaic of lateral transfer events within a constant genome scaffold. These differences result in an extraordinary diversity of host-ranges and pathogenic presentations between strains. Known virulence functions are encoded primarily within these laterally transferred regions. However, despite 30+ years of intensive study, the functions of most genes within these important regions are still unknown. We are in the process of rectifying this gap in knowledge. Objective. Understand the evolution of pathogenesis in Salmonella with the objective of generating principles applicable to other diseases, allowing new methods of treatment, diagnostics, and also exploitation of avirulent strains for human needs. Approaches. A. We have sequenced strains used in laboratory research and are now sequencing over 300 more strains

that capture the diversity of the species. Understanding sequence diversity allows steps in evolution to be better understood and allows development of DNA typing methods that correlate better with infectious manifestations.

B. We have developed high-throughput sequencing methods for:

RNA expression, including capturing expression from pathogens in host tissue. Screening promoter-GFP libraries for all promoters. Studying the fitness of all genomic regions, simultaneously, in animal gut during interaction

with the microbiome, systemic infection, and the environment. C. In collaboration with Helene Andrews-Polymenis, we have constructed a collection of specific gene

knockouts in almost all genes in Salmonella Typhimurium, as well as multi-gene deletions covering most of the genome. This tool allows us to avoid the bottlenecks in infection that preclude most genetic approaches.

D. We have begun a program in comparative systems biology using Salmonella Enteritidis, which has recently become the most prevalent clinical serovar, replacing Typhimurium.

E. Almost all pathogenic enterobacteria have one or more prophage in their genome, which are poised to

activate during DNA damage. The host uses DNA damage as a major defense mechanism. We have recently begun a program to understand this tension. We believe that either the host or pathogen, or both, may exploit phage induction in the infection process.

Program 2: Salmonella as a therapeutic delivery agent in cancer. Background. Harmless live vaccine strains of Salmonella naturally accumulate 1000X in tumors and sometimes kill tumor cells leading to cures. Salmonella can be used to deliver therapeutic agents, such as enzymes for drug metabolism and cytokines. Objective. Improve upon the natural ability of Salmonella to kill tumors. Improve the ability of Salmonella to delivery therapeutics. Understand why Salmonella accumulates in tumors and use this information to create better targeting and synergistic treatments. Approaches. We are using high-throughput methods, many of our own devising: A. Identify avirulent bacterial mutants that grow better in tumors than in other organs.

B. Identify bacterial promoters and transcripts active in tumors to:

Express therapeutics. Better understand what the bacterium senses in the tumor to better engineer the bacterium to

target tumors and adversely affect tumor growth.

C. Identify transcripts in the host tumor that react to the presence of bacteria, to better understand this interaction and find synergistic treatments that may make therapy more effective.

D. Experiments in companion animals would be a natural next step for this therapeutic. Program 3: Biomarkers for prostate cancer recurrence. Background. Prostate cancer is the most common cancer in men. 70% of 70 year olds have some evidence of disease at autopsy. However, the majority of prostate cancers do not lead to death even if left untreated. Most cases are treated, nevertheless, because there is no test for accurate identification of indolent versus aggressive cases. More than 100,000 men are treated unnecessarily each year in the US, at a cost of billions of dollars, and with some side-effects in most cases. Objective. Develop prognostic tests to accurately define those patients with progressive disease, so they can be targeted for early aggressive treatment. Approaches. In collaboration with Dan Mercola, we accumulated clinical data over decades for hundreds of consented patients. We previously showed that stroma responds to the presence of tumor and developed methods that assign predictive markers to tumor or adjacent reactive tissues. A. Testing prognostic RNA markers from tumor.

B. Testing prognostic RNA markers from tumor-adjacent stroma. The idea is that stroma, being

genetically normal, may be a more stable observer of aggressiveness. C. Expression of the corresponding biomarker proteins are generally correlated with RNA expression. In

collaboration with companies, we are working on multiplex immunofluorescence. D. Tissue microarrays developed to potentially accelerate validation. E. Potentially, post-translational protein modifications may be even more sensitive prognosticators.

Program 4: Cancer Genomics and Personalized Medicine. A. I am working with CHOC (Children’s Hospital of Orange County) as a part of the Scientific Advisory

Board and as a member of their Tumor Board, on a recently funded project to sequence childhood cancers. We hope to leverage this infrastructure to generalize the approach to adult cancers at UCI to identify:

Inherited polymorphisms and cancer-mutated sites affecting pharmacological responsiveness. Mutations in the rapidly expanding list of “druggable” pathways for patients that have failed

standard of care. B. Efforts are well advanced with Dr. Mercola to develop a self-sustaining biorepository in the

Department of Pathology of fresh frozen tissues from all cancers at UCI, in excess of those immediately needed for pathology. This initiative is a subset of the efforts by the Dean of Medicine to build up personalized medicine at UCI and also has the support of the Cancer Center. The biorepository would be used for any number of assays that required fresh frozen tissues and could also be extended to samples from other diseases. While the repository would be for clinical purposes, it would also encompass research purposes, with lead research investigators taking control and responsibility for subsets of tissues. In tandem with these efforts there is a need to dramatically improve molecular diagnostics available at UCI.

C. We are working with Medical Informatics to encourage the development of an “honest broker” system

that would greatly enhance the utility of the biorepository and accompanying clinical information, for the entire medical school, while ensuring Pathology retains a central role in assessment of clinical tissues.

D. I have been made a team leader in the Cancer Prevention and Prognosis Research Program at UCI Chao

Family Comprehensive Cancer Center, tasked with helping to improve the integration of this program as the Cancer Center prepares for a competitive renewal grant submission. To take on this role I resigned my position in the UCSD Cancer Center.

Other UCI programs. A. Among our early stage projects is the exploitation of the fact that some nucleosomes are precisely

positioned in the genome, and that this positioning is cell-type specific. In collaboration with Liz Chao, an adjunct member of the department, we are studying the release of nucleosomal DNA by dying cancer cells to identify DNA regions that are consistently protected and might be better targets for cancer detection assays (microsatellites, DNA methylation, etc., in fluids such as blood.

B. We are putting together a multi-investigator effort, to study genes of unknown function in Salmonella

using a combination of studies of protein-protein interactions, screens of mutants under hundreds of different conditions, screens of invasion, and systems biology to stitch together these heterogeneous data.